Detailed view for Tb927.5.4030

Basic information

TDR Targets ID: 20628
Trypanosoma brucei, U6 snRNA-associated Sm-like protein LSm7p
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.2792 | Length (AA): 92 | MW (Da): 10214 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

Druggability Group : DG1

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF01423   LSM domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0030629   U6 snRNA 3'-end binding  
GO:0000398   nuclear mRNA splicing, via spliceosome  
GO:0005634   nucleus  

Metabolic Pathways

RNA degradation (KEGG)
Spliceosome (KEGG)

Structural information

Modbase 3D models:

There are 5 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
14 84 4c92 (G) 26 108 38.00 0.000000000025 1 1.28704 -0.72
17 90 4m77 (A) 4 97 30.00 0 1 1.10785 -0.25
17 82 1d3b (B) 8 84 32.00 0 1 1.03189 -0.89
18 81 1n9r (A) 19 84 28.00 0.00000000054 1 1.09695 -0.68
27 62 4emk (A) 21 49 52.00 0.92 0.62 0.605204 1.16

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Procyclic. Siegel TN
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_128343)

Species Accession Gene Product
Arabidopsis thaliana AT2G03870   U6 snRNA-associated Sm-like protein LSm7
Babesia bovis BBOV_III001070   LSM domain containing protein
Brugia malayi Bm1_31505   U6 snRNA-associated Sm-like protein LSm7
Caenorhabditis elegans CELE_ZK593.7   Protein LSM-7
Cryptosporidium parvum cgd7_3520   hypothetical protein
Dictyostelium discoideum DDB_G0289499   LSM domain-containing protein
Drosophila melanogaster Dmel_CG13277   CG13277 gene product from transcript CG13277-RC
Entamoeba histolytica EHI_025840   LSM domain containing protein
Homo sapiens ENSG00000130332   LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)
Leishmania braziliensis LbrM.26.0020   Lsm7p protein, putative
Leishmania donovani LdBPK_260010.1   Lsm7p protein, putative
Leishmania infantum LinJ.26.0010   Lsm7p protein, putative
Leishmania major LmjF.26.0005   Lsm7p protein, putative
Leishmania mexicana LmxM.26.0005   Lsm7p protein, putative
Loa Loa (eye worm) LOAG_01816   hypothetical protein
Mus musculus ENSMUSG00000035215   LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)
Neospora caninum NCLIV_014070   u6 snRNA-associated Sm-like protein, putative
Oryza sativa 4344803   Os08g0177700
Plasmodium berghei PBANKA_0607600   U6 snRNA-associated Sm-like protein LSm7, putative
Plasmodium falciparum PF3D7_1209200   U6 snRNA-associated Sm-like protein LSm7, putative
Plasmodium knowlesi PKNH_1309100   U6 snRNA-associated Sm-like protein LSm7, putative
Plasmodium vivax PVX_084490   U6 snRNA-associated Sm-like protein LSm7, putative
Plasmodium yoelii PY03614   u6 snRNA-associated sm-like protein lsm7
Saccharomyces cerevisiae YNL147W   Sm-like protein LSM7
Schmidtea mediterranea mk4.002749.00  
Trypanosoma brucei gambiense Tbg972.5.5570   U6 snRNA-associated Sm-like protein LSm7p
Trypanosoma brucei Tb927.5.4030   U6 snRNA-associated Sm-like protein LSm7p
Trypanosoma congolense TcIL3000_5_4560   U6 snRNA-associated Sm-like protein LSm7p, putative
Trypanosoma cruzi TcCLB.506855.209   U6 snRNA-associated Sm-like protein LSm7p
Trypanosoma cruzi TcCLB.503479.49   U6 snRNA-associated Sm-like protein LSm7p
Toxoplasma gondii TGME49_286560   U6 snRNA-associated Sm family protein
Theileria parva TP03_0732   U6 snRNA-associated protein, putative

Essentiality

Tb927.5.4030 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.5.4030 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.5.4030 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.5.4030 this record Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.5.4030 this record Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_ZK593.7 Caenorhabditis elegans embryonic lethal wormbase
CELE_ZK593.7 Caenorhabditis elegans larval arrest wormbase
CELE_ZK593.7 Caenorhabditis elegans slow growth wormbase
CELE_ZK593.7 Caenorhabditis elegans sterile wormbase
YNL147W Saccharomyces cerevisiae inviable yeastgenome
TGME49_286560 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) increased (PATO:0000470) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: increased cell proliferation (significant gain of fitness) in bloodstream forms (stage 3 days). References: 21363968
cell proliferation (GO:0008283) normal (PATO:0000461) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) increased (PATO:0000470) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: increased cell proliferation (significant gain of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

1 literature reference was collected for this gene.

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Gene identifier Tb927.5.4030 (Trypanosoma brucei), U6 snRNA-associated Sm-like protein LSm7p
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